Index

_

__call__() (orangecontrib.bio.utils.stats.Binomial method) (orangecontrib.bio.utils.stats.Hypergeometric method) __contains__() (orangecontrib.bio.go.Ontology method) __getitem__() (orangecontrib.bio.go.Ontology method)

__init__() (orangecontrib.bio.dicty.CacheSQLite method) (orangecontrib.bio.dicty.DictyExpress method) (orangecontrib.bio.dicty.PIPAx method) __iter__() (orangecontrib.bio.go.Ontology method) __len__() (orangecontrib.bio.go.Ontology method)

A

aaseq (orangecontrib.bio.kegg.databases.GeneEntry attribute) add() (orangecontrib.bio.dicty.CacheSQLite method) (orangecontrib.bio.go.Annotations method) add_annotation() (orangecontrib.bio.go.Annotations method) add_header_tag() (orangecontrib.bio.ontology.OBOOntology method) add_object() (orangecontrib.bio.ontology.OBOOntology method) add_tag() (orangecontrib.bio.ontology.OBOObject method) all_edges() (orangecontrib.bio.ppi.BioGRID method) (orangecontrib.bio.ppi.PPIDatabase method) (orangecontrib.bio.ppi.STRING method) (orangecontrib.bio.ppi.STRINGDetailed method) all_edges_annotated() (orangecontrib.bio.ppi.BioGRID method) (orangecontrib.bio.ppi.PPIDatabase method) all_genes() (in module orangecontrib.bio.gene.homology) all_genes_inParanoid() (in module orangecontrib.bio.gene.homology) all_reac (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) annotation (orangecontrib.bio.kegg.databases.GenomeEntry attribute) Annotation_Extension (orangecontrib.bio.go.AnnotationRecord attribute) annotationOptions() (orangecontrib.bio.dicty.DictyExpress method) AnnotationRecord (class in orangecontrib.bio.go) Annotations (class in orangecontrib.bio.go) annotations (orangecontrib.bio.go.Annotations attribute)

annotations() (orangecontrib.bio.dicty.DictyExpress method) annotationTypes() (orangecontrib.bio.dicty.DictyExpress method) append() (orangecontrib.bio.go.Annotations method) array_data() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) array_data_file() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) array_data_matrix() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) array_data_matrix_file() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) ArrayDesign (class in orangecontrib.bio.arrayexpress) ArrayExpressConnection (class in orangecontrib.bio.arrayexpress) Aspect (orangecontrib.bio.go.AnnotationRecord attribute) assay() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) assay_name() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) Assigned_By (orangecontrib.bio.go.AnnotationRecord attribute) atom (orangecontrib.bio.kegg.databases.CompoundEntry attribute) Attribute (class in orangecontrib.bio.biomart) attributes() (orangecontrib.bio.biomart.BioMartDataset method)

B

batch_get() (orangecontrib.bio.kegg.databases.DBDataBase method) Binomial (class in orangecontrib.bio.utils.stats) binomial distribution BioGRID (class in orangecontrib.bio.ppi) BioMartConnection (class in orangecontrib.bio.biomart) BioMartDatabase (class in orangecontrib.bio.biomart) BioMartDataset (class in orangecontrib.bio.biomart)

BioMartQuery (class in orangecontrib.bio.biomart) BioMartRegistry (class in orangecontrib.bio.biomart) BioMartVirtualSchema (class in orangecontrib.bio.biomart) bond (orangecontrib.bio.kegg.databases.CompoundEntry attribute) Bonferroni Bonferroni() (in module orangecontrib.bio.utils.stats) brite (orangecontrib.bio.kegg.databases.CompoundEntry attribute)

C

CacheSQLite (class in orangecontrib.bio.dicty) child_edges() (orangecontrib.bio.ontology.OBOOntology method) child_terms() (orangecontrib.bio.ontology.OBOOntology method) chromosome (orangecontrib.bio.kegg.databases.GenomeEntry attribute) class_ (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) (orangecontrib.bio.kegg.databases.GeneEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) clear() (orangecontrib.bio.dicty.CacheSQLite method) cname() (orangecontrib.bio.geneset.GeneSet method) collections() (in module orangecontrib.bio.geneset) comment (orangecontrib.bio.kegg.databases.CompoundEntry attribute) (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) (orangecontrib.bio.kegg.databases.GenomeEntry attribute) commit() (orangecontrib.bio.dicty.CacheSQLite method)

common_hierarchy() (orangecontrib.bio.geneset.GeneSets method) common_org() (orangecontrib.bio.geneset.GeneSets method) common_taxids() (in module orangecontrib.bio.taxonomy) Compound (class in orangecontrib.bio.kegg.databases) compound (orangecontrib.bio.kegg.databases.PathwayEntry attribute) CompoundEntry (class in orangecontrib.bio.kegg.databases) configuration() (orangecontrib.bio.biomart.BioMartDataset method) contains() (orangecontrib.bio.dicty.CacheSQLite method) count() (orangecontrib.bio.biomart.BioMartDataset method)

D

D. dictyostelium mutants data_source (orangecontrib.bio.kegg.databases.GenomeEntry attribute) databases() (orangecontrib.bio.biomart.BioMartRegistry method) (orangecontrib.bio.biomart.BioMartVirtualSchema method) dataset() (orangecontrib.bio.biomart.BioMartRegistry method) (orangecontrib.bio.biomart.BioMartVirtualSchema method) dataset_attributes() (orangecontrib.bio.biomart.BioMartDatabase method) dataset_filters() (orangecontrib.bio.biomart.BioMartDatabase method) dataset_query() (orangecontrib.bio.biomart.BioMartDatabase method) DatasetConfig (class in orangecontrib.bio.biomart) datasets() (orangecontrib.bio.biomart.BioMartDatabase method) (orangecontrib.bio.biomart.BioMartRegistry method) (orangecontrib.bio.biomart.BioMartVirtualSchema method) Date (orangecontrib.bio.go.AnnotationRecord attribute) DB (orangecontrib.bio.go.AnnotationRecord attribute) (orangecontrib.bio.kegg.databases.DBDataBase attribute) DB_Object_ID (orangecontrib.bio.go.AnnotationRecord attribute) DB_Object_Name (orangecontrib.bio.go.AnnotationRecord attribute) DB_Object_Symbol (orangecontrib.bio.go.AnnotationRecord attribute) DB_Object_Synonym (orangecontrib.bio.go.AnnotationRecord attribute) DB_Object_Type (orangecontrib.bio.go.AnnotationRecord attribute) DB_Reference (orangecontrib.bio.go.AnnotationRecord attribute) DBDataBase (class in orangecontrib.bio.kegg.databases) DBEntry (class in orangecontrib.bio.kegg.entry)

DBGETEntryParser (class in orangecontrib.bio.kegg.entry.parser) dblinks (orangecontrib.bio.kegg.databases.CompoundEntry attribute) (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) (orangecontrib.bio.kegg.databases.GeneEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) def_ (orangecontrib.bio.go.Term attribute) defined_slims_subsets() (orangecontrib.bio.go.Ontology method) definition (orangecontrib.bio.kegg.databases.GeneEntry attribute) (orangecontrib.bio.kegg.databases.GenomeEntry attribute) (orangecontrib.bio.kegg.databases.ReactionEntry attribute) derived_array_data() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) derived_array_data_file() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) derived_array_data_matrix() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) derived_array_data_matrix_file() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) description (orangecontrib.bio.biomart.Attribute attribute) (orangecontrib.bio.biomart.Filter attribute) (orangecontrib.bio.geneset.GeneSet attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) DictyExpress (class in orangecontrib.bio.dicty) DictyMutant (class in orangecontrib.bio.dicty.phenotypes) DictyMutants (class in orangecontrib.bio.dicty.phenotypes) disease (orangecontrib.bio.kegg.databases.GeneEntry attribute) (orangecontrib.bio.kegg.databases.GenomeEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) disease_genes() (in module orangecontrib.bio.omim) diseases() (in module orangecontrib.bio.omim) download_data() (orangecontrib.bio.ppi.BioGRID class method) (orangecontrib.bio.ppi.PPIDatabase class method) (orangecontrib.bio.ppi.STRING class method) drug (orangecontrib.bio.kegg.databases.PathwayEntry attribute) drug_target (orangecontrib.bio.kegg.databases.GeneEntry attribute)

E

edge_types() (orangecontrib.bio.ontology.OBOOntology method) edges() (orangecontrib.bio.ppi.BioGRID method) (orangecontrib.bio.ppi.PPIDatabase method) (orangecontrib.bio.ppi.STRING method) (orangecontrib.bio.ppi.STRINGDetailed method) edges_annotated() (orangecontrib.bio.ppi.BioGRID method) (orangecontrib.bio.ppi.PPIDatabase method) entry (orangecontrib.bio.kegg.databases.CompoundEntry attribute) (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) (orangecontrib.bio.kegg.databases.GeneEntry attribute) (orangecontrib.bio.kegg.databases.GenomeEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) (orangecontrib.bio.kegg.databases.ReactionEntry attribute) ENTRY_END (orangecontrib.bio.kegg.entry.parser.DBGETEntryParser attribute) entry_key (orangecontrib.bio.kegg.entry.DBEntry attribute) ENTRY_START (orangecontrib.bio.kegg.entry.parser.DBGETEntryParser attribute) ENTRY_TYPE (orangecontrib.bio.kegg.databases.DBDataBase attribute) (orangecontrib.bio.kegg.databases.Genome attribute) Enzyme (class in orangecontrib.bio.kegg.databases) enzyme (orangecontrib.bio.kegg.databases.CompoundEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) (orangecontrib.bio.kegg.databases.ReactionEntry attribute) EnzymeEntry (class in orangecontrib.bio.kegg.databases)

equation (orangecontrib.bio.kegg.databases.ReactionEntry attribute) essential_taxids() (in module orangecontrib.bio.taxonomy) Evidence_Code (orangecontrib.bio.go.AnnotationRecord attribute) exact_mass (orangecontrib.bio.kegg.databases.CompoundEntry attribute) explain() (orangecontrib.bio.gene.Matcher method) extend() (orangecontrib.bio.go.Annotations method) extract() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) extract_name() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) extract_network() (orangecontrib.bio.ppi.BioGRID method) (orangecontrib.bio.ppi.PPIDatabase method) (orangecontrib.bio.ppi.STRING method) (orangecontrib.bio.ppi.STRINGDetailed method) extract_sub_graph() (orangecontrib.bio.go.Ontology method) extract_super_graph() (orangecontrib.bio.go.Ontology method)

F

FDR FDR() (in module orangecontrib.bio.utils.stats) Filter (class in orangecontrib.bio.biomart) filters() (orangecontrib.bio.biomart.BioMartDataset method) find() (orangecontrib.bio.kegg.databases.DBDataBase method) format (orangecontrib.bio.biomart.Attribute attribute)

format() (orangecontrib.bio.kegg.entry.DBEntry method) format_query() (orangecontrib.bio.arrayexpress.ArrayExpressConnection method) format_stanza() (orangecontrib.bio.ontology.OBOObject method) formula (orangecontrib.bio.kegg.databases.CompoundEntry attribute) from_string() (orangecontrib.bio.go.AnnotationRecord class method) from_taxid() (in module orangecontrib.bio.kegg)

G

GDS (class in orangecontrib.bio.geo) GDSInfo (class in orangecontrib.bio.geo) Gene Expression Omnibus gene info gene matching gene name matching gene set gene sets gene_aliases() (orangecontrib.bio.kegg.Organism method) gene_annotations (orangecontrib.bio.go.Annotations attribute) gene_diseases() (in module orangecontrib.bio.omim) gene_mutants() (in module orangecontrib.bio.dicty.phenotypes) Gene_Product_Form_ID (orangecontrib.bio.go.AnnotationRecord attribute) GeneEntry (class in orangecontrib.bio.kegg.databases) Genes (class in orangecontrib.bio.kegg.databases) genes (orangecontrib.bio.geneset.GeneSet attribute) (orangecontrib.bio.kegg.Organism attribute) (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) genes() (in module orangecontrib.bio.dicty.phenotypes) (in module orangecontrib.bio.omim) GeneSet (class in orangecontrib.bio.geneset) GeneSets (class in orangecontrib.bio.geneset)

Genome (class in orangecontrib.bio.kegg.databases) GenomeEntry (class in orangecontrib.bio.kegg.databases) genomes() (orangecontrib.bio.dicty.PIPAx method) GEO get() (orangecontrib.bio.dicty.CacheSQLite method) (orangecontrib.bio.kegg.databases.DBDataBase method) get_all_annotations() (orangecontrib.bio.go.Annotations method) get_all_genes() (orangecontrib.bio.go.Annotations method) get_annotated_terms() (orangecontrib.bio.go.Annotations method) get_data() (orangecontrib.bio.biomart.BioMartDataset method) (orangecontrib.bio.dicty.DictyExpress method) (orangecontrib.bio.dicty.PIPAx method) get_enriched_pathways() (orangecontrib.bio.kegg.Organism method) get_enriched_terms() (orangecontrib.bio.go.Annotations method) get_entry() (orangecontrib.bio.kegg.databases.DBDataBase method) get_gene_names_translator() (orangecontrib.bio.go.Annotations method) get_image() (orangecontrib.bio.kegg.pathway.Pathway method) get_pathways_by_genes() (orangecontrib.bio.kegg.Organism method) get_text() (orangecontrib.bio.kegg.databases.DBDataBase method) get_unique_gene_ids() (orangecontrib.bio.kegg.Organism method) getdata() (orangecontrib.bio.geo.GDS method) GO_ID (orangecontrib.bio.go.AnnotationRecord attribute)

H

hierarchies() (orangecontrib.bio.geneset.GeneSets method) hierarchy (orangecontrib.bio.geneset.GeneSet attribute) homolog() (in module orangecontrib.bio.gene.homology) homologs() (in module orangecontrib.bio.gene.homology)

hybridization() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) hybridization_name() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) Hypergeometric (class in orangecontrib.bio.utils.stats) hypergeometric distribution

I

id (orangecontrib.bio.geneset.GeneSet attribute) (orangecontrib.bio.go.Term attribute) (orangecontrib.bio.ontology.OBOObject attribute) ids() (orangecontrib.bio.ppi.BioGRID method) (orangecontrib.bio.ppi.PPIDatabase method) (orangecontrib.bio.ppi.STRING method) (orangecontrib.bio.ppi.STRINGDetailed method) image (orangecontrib.bio.kegg.pathway.Pathway attribute) image() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) image_file() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) init_db() (orangecontrib.bio.ppi.BioGRID class method) init_db_index() (orangecontrib.bio.ppi.BioGRID method) Instance (class in orangecontrib.bio.ontology) instances() (orangecontrib.bio.ontology.OBOOntology method)

internal_name (orangecontrib.bio.biomart.Attribute attribute) (orangecontrib.bio.biomart.Filter attribute) internalName (orangecontrib.bio.biomart.Attribute attribute) InvestigationDesign (class in orangecontrib.bio.arrayexpress) is_a (orangecontrib.bio.go.Term attribute) is_annonymous (orangecontrib.bio.ontology.OBOObject attribute) items() (orangecontrib.bio.kegg.databases.DBDataBase method) iteritems() (orangecontrib.bio.kegg.databases.DBDataBase method) iterkeys() (orangecontrib.bio.kegg.databases.DBDataBase method) itervalues() (orangecontrib.bio.kegg.databases.DBDataBase method)

K

KEGGOrganism (in module orangecontrib.bio.kegg) keys() (orangecontrib.bio.kegg.databases.DBDataBase method)

keywords (orangecontrib.bio.kegg.databases.GenomeEntry attribute) ko_pathway (orangecontrib.bio.kegg.databases.PathwayEntry attribute)

L

labeled_extract() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) labeled_extract_name() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) lineage() (in module orangecontrib.bio.taxonomy) link (orangecontrib.bio.geneset.GeneSet attribute) (orangecontrib.bio.kegg.pathway.Pathway attribute) links() (orangecontrib.bio.biomart.BioMartVirtualSchema method)

links_between() (orangecontrib.bio.biomart.BioMartRegistry method) (orangecontrib.bio.biomart.BioMartVirtualSchema method) list() (orangecontrib.bio.dicty.CacheSQLite method) (orangecontrib.bio.kegg.pathway.Pathway class method) list_all() (in module orangecontrib.bio.geneset) list_pathways() (orangecontrib.bio.kegg.Organism method) load() (orangecontrib.bio.ontology.OBOOntology method)

M

mappings() (orangecontrib.bio.dicty.PIPAx method) mart() (orangecontrib.bio.biomart.BioMartRegistry method) marts() (orangecontrib.bio.biomart.BioMartRegistry method) (orangecontrib.bio.biomart.BioMartVirtualSchema method) match() (orangecontrib.bio.gene.Matcher method) Matcher (class in orangecontrib.bio.gene) matcher() (in module orangecontrib.bio.gene) MatcherAliasesDictyBase (class in orangecontrib.bio.gene) MatcherAliasesEnsembl (class in orangecontrib.bio.gene) MatcherAliasesGO (class in orangecontrib.bio.gene) MatcherAliasesKEGG (class in orangecontrib.bio.gene) MatcherAliasesNCBI (class in orangecontrib.bio.gene)

MatcherDirect (class in orangecontrib.bio.gene) matching microarray data sets module (orangecontrib.bio.kegg.databases.GeneEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) mol_weight (orangecontrib.bio.kegg.databases.CompoundEntry attribute) motif (orangecontrib.bio.kegg.databases.GeneEntry attribute) mutant phenotypes mutant_genes() (in module orangecontrib.bio.dicty.phenotypes) mutant_phenotypes() (in module orangecontrib.bio.dicty.phenotypes) mutants() (in module orangecontrib.bio.dicty.phenotypes)

N

name (orangecontrib.bio.biomart.Attribute attribute) (orangecontrib.bio.biomart.Filter attribute) (orangecontrib.bio.geneset.GeneSet attribute) (orangecontrib.bio.kegg.databases.CompoundEntry attribute) (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) (orangecontrib.bio.kegg.databases.GeneEntry attribute) (orangecontrib.bio.kegg.databases.GenomeEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) (orangecontrib.bio.kegg.databases.ReactionEntry attribute) (orangecontrib.bio.kegg.pathway.Pathway attribute) (orangecontrib.bio.ontology.OBOObject attribute) name() (in module orangecontrib.bio.taxonomy) named_slims_subset() (orangecontrib.bio.go.Ontology method) namespace (orangecontrib.bio.go.Term attribute) NCBI, [1], [2]

normalization() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) normalization_name() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) ntseq (orangecontrib.bio.kegg.databases.GeneEntry attribute) number (orangecontrib.bio.kegg.pathway.Pathway attribute)

O

objects() (orangecontrib.bio.dicty.DictyExpress method) OBOObject (class in orangecontrib.bio.ontology) OBOOntology (class in orangecontrib.bio.ontology) OBOParser (class in orangecontrib.bio.ontology) OMIM Ontology (class in orangecontrib.bio.go) ontology (orangecontrib.bio.go.Annotations attribute) open_file() (orangecontrib.bio.arrayexpress.ArrayExpressConnection method) orangecontrib.bio.dicty.phenotypes (module) orangecontrib.bio.geneset (module) orangecontrib.bio.go (module) orangecontrib.bio.kegg (module)

orangecontrib.bio.ontology (module) org (orangecontrib.bio.kegg.Organism attribute) (orangecontrib.bio.kegg.pathway.Pathway attribute) org_code_to_entry_key() (orangecontrib.bio.kegg.databases.Genome method) Organism (class in orangecontrib.bio.kegg) organism (orangecontrib.bio.geneset.GeneSet attribute) (orangecontrib.bio.kegg.databases.GeneEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) organism_code (orangecontrib.bio.kegg.databases.GenomeEntry attribute) organism_name_search() (in module orangecontrib.bio.kegg) organisms() (orangecontrib.bio.ppi.PPIDatabase method) (orangecontrib.bio.ppi.STRING method) (orangecontrib.bio.ppi.STRINGDetailed method) original_db (orangecontrib.bio.kegg.databases.GenomeEntry attribute) orthologs() (in module orangecontrib.bio.gene.homology) orthology (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) (orangecontrib.bio.kegg.databases.GeneEntry attribute) other_names() (in module orangecontrib.bio.taxonomy)

P

p_value() (orangecontrib.bio.utils.stats.Binomial method) (orangecontrib.bio.utils.stats.Hypergeometric method) parent_edges() (orangecontrib.bio.ontology.OBOOntology method) parent_terms() (orangecontrib.bio.ontology.OBOOntology method) parse() (orangecontrib.bio.biomart.BioMartRegistry class method) (orangecontrib.bio.kegg.entry.DBEntry method) (orangecontrib.bio.ontology.OBOParser method) parse_stanza() (orangecontrib.bio.ontology.OBOObject class method) Pathway (class in orangecontrib.bio.kegg.databases) (class in orangecontrib.bio.kegg.pathway) pathway (orangecontrib.bio.kegg.databases.CompoundEntry attribute) (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) (orangecontrib.bio.kegg.databases.GeneEntry attribute) pathway_map (orangecontrib.bio.kegg.databases.PathwayEntry attribute) PathwayEntry (class in orangecontrib.bio.kegg.databases) pathways() (in module orangecontrib.bio.kegg) (orangecontrib.bio.kegg.Organism method)

phenotype_mutants() (in module orangecontrib.bio.dicty.phenotypes) phenotypes phenotypes() (in module orangecontrib.bio.dicty.phenotypes) PIPAx (class in orangecontrib.bio.dicty) plasmid (orangecontrib.bio.kegg.databases.GenomeEntry attribute) position (orangecontrib.bio.kegg.databases.GeneEntry attribute) PPIDatabase (class in orangecontrib.bio.ppi) pre_cache() (orangecontrib.bio.kegg.databases.DBDataBase method) product (orangecontrib.bio.kegg.databases.EnzymeEntry attribute)

Q

Qualifier (orangecontrib.bio.go.AnnotationRecord attribute) query() (orangecontrib.bio.biomart.BioMartRegistry method) (orangecontrib.bio.biomart.BioMartVirtualSchema method) query_experiment() (orangecontrib.bio.arrayexpress.ArrayExpressConnection method) query_experiments() (in module orangecontrib.bio.arrayexpress)

query_files() (in module orangecontrib.bio.arrayexpress) (orangecontrib.bio.arrayexpress.ArrayExpressConnection method) query_url() (orangecontrib.bio.arrayexpress.ArrayExpressConnection method) query_url_experiments() (orangecontrib.bio.arrayexpress.ArrayExpressConnection method) query_url_files() (orangecontrib.bio.arrayexpress.ArrayExpressConnection method)

R

Reaction (class in orangecontrib.bio.kegg.databases) reaction (orangecontrib.bio.kegg.databases.CompoundEntry attribute) (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) ReactionEntry (class in orangecontrib.bio.kegg.databases) reference (orangecontrib.bio.kegg.databases.CompoundEntry attribute) (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) (orangecontrib.bio.kegg.databases.GenomeEntry attribute) (orangecontrib.bio.kegg.databases.PathwayEntry attribute) register() (in module orangecontrib.bio.geneset) rel_pathway (orangecontrib.bio.kegg.databases.PathwayEntry attribute) related (orangecontrib.bio.go.Term attribute)

related_objects() (orangecontrib.bio.ontology.OBOObject method) related_terms() (orangecontrib.bio.ontology.OBOOntology method) relations() (orangecontrib.bio.ontology.OBOOntology method) remark (orangecontrib.bio.kegg.databases.CompoundEntry attribute) result_types() (orangecontrib.bio.dicty.PIPAx method) results_list() (orangecontrib.bio.dicty.PIPAx method) root_terms() (orangecontrib.bio.ontology.OBOOntology method)

S

sample() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) sample_annotations() (orangecontrib.bio.geo.GDS method) sample_name() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) sample_to_class() (orangecontrib.bio.geo.GDS method) sample_types() (orangecontrib.bio.geo.GDS method) SampleDataRelationship (class in orangecontrib.bio.arrayexpress) scan() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) scan_name() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) search() (in module orangecontrib.bio.taxonomy) (orangecontrib.bio.dicty.DictyExpress method) (orangecontrib.bio.kegg.databases.Genome method) search_id() (orangecontrib.bio.ppi.BioGRID method) (orangecontrib.bio.ppi.PPIDatabase method) SECTION_END (orangecontrib.bio.kegg.entry.parser.DBGETEntryParser attribute) SECTION_START (orangecontrib.bio.kegg.entry.parser.DBGETEntryParser attribute) set_hierarchy() (orangecontrib.bio.geneset.GeneSets method) set_slims_subset() (orangecontrib.bio.go.Ontology method) set_targets() (orangecontrib.bio.gene.Matcher method) slims_for_term() (orangecontrib.bio.go.Ontology method)

source() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) source_name() (orangecontrib.bio.arrayexpress.SampleDataRelationship method) split_by_hierarchy() (orangecontrib.bio.geneset.GeneSets method) statistics (orangecontrib.bio.kegg.databases.GenomeEntry attribute) STRING (class in orangecontrib.bio.ppi) STRINGDetailed (class in orangecontrib.bio.ppi) structure (orangecontrib.bio.kegg.databases.GeneEntry attribute) sub_terms() (orangecontrib.bio.ontology.OBOOntology method) SUBSECTION_END (orangecontrib.bio.kegg.entry.parser.DBGETEntryParser attribute) SUBSECTION_START (orangecontrib.bio.kegg.entry.parser.DBGETEntryParser attribute) substrate (orangecontrib.bio.kegg.databases.EnzymeEntry attribute) super_terms() (orangecontrib.bio.ontology.OBOOntology method) synonyms() (orangecontrib.bio.ppi.BioGRID method) (orangecontrib.bio.ppi.PPIDatabase method) (orangecontrib.bio.ppi.STRING method) (orangecontrib.bio.ppi.STRINGDetailed method) synonyms_with_source() (orangecontrib.bio.ppi.STRING method) (orangecontrib.bio.ppi.STRINGDetailed method) sysname (orangecontrib.bio.kegg.databases.EnzymeEntry attribute)

T

tag_count() (orangecontrib.bio.ontology.OBOObject method) tags() (orangecontrib.bio.ontology.OBOObject method) taxid (orangecontrib.bio.kegg.databases.GenomeEntry attribute) taxids() (in module orangecontrib.bio.taxonomy) Taxon (orangecontrib.bio.go.AnnotationRecord attribute) taxonomy (orangecontrib.bio.kegg.databases.GenomeEntry attribute) Term (class in orangecontrib.bio.go) (class in orangecontrib.bio.ontology) term() (orangecontrib.bio.ontology.OBOOntology method) term_anotations (orangecontrib.bio.go.Annotations attribute) term_by_name() (orangecontrib.bio.ontology.OBOOntology method) terms() (orangecontrib.bio.ontology.OBOOntology method)

TEXT (orangecontrib.bio.kegg.entry.parser.DBGETEntryParser attribute) title (orangecontrib.bio.kegg.pathway.Pathway attribute) to_graphviz() (orangecontrib.bio.ontology.OBOOntology method) to_network() (orangecontrib.bio.ontology.OBOOntology method) to_networkx() (orangecontrib.bio.ontology.OBOOntology method) to_odict() (orangecontrib.bio.geneset.GeneSet method) (orangecontrib.bio.geneset.GeneSets method) to_taxid() (in module orangecontrib.bio.kegg) transform_tag() (orangecontrib.bio.arrayexpress.InvestigationDesign method) (orangecontrib.bio.arrayexpress.SampleDataRelationship method) Typedef (class in orangecontrib.bio.ontology) typedefs() (orangecontrib.bio.ontology.OBOOntology method)

U

umatch() (orangecontrib.bio.gene.Matcher method)

update() (orangecontrib.bio.ontology.OBOObject method) (orangecontrib.bio.ontology.OBOOntology method)

V

values (orangecontrib.bio.biomart.Filter attribute) values() (orangecontrib.bio.kegg.databases.DBDataBase method)

virtual_schema() (orangecontrib.bio.biomart.BioMartRegistry method) virtual_schemas() (orangecontrib.bio.biomart.BioMartRegistry method)

W

With_From (orangecontrib.bio.go.AnnotationRecord attribute)

write() (orangecontrib.bio.ontology.OBOOntology method)